Abstract 508: Clinical significance of a negative elongation factor-E (NELF-E) single nucleotide polymorphism in hepatocellular carcinoma (HCC)
Authors: Ryan Lamm, Anna Barry-Wolbers, Kai Zhang, Keyur Patel, Hien T. Dang
Journal: Cancer Research (2022)

Abstract Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer deaths worldwide. Multiple causative etiologies, such as hepatitis B and C (HBV/HCV), alcohol, and non-alcoholic steatohepatitis (NASH), lead to heterogeneous tumor microenvironments and modest at best responses to available therapy. Previous work has identified that high levels of negative elongation factor-E (NELF-E), part of the transcription regulating NELF complex, promote tumor progression and significantly lower overall survival in more than 38% of HCC tumors. Further studies identified a germline single nucleotide polymorphism (SNP) of NELF-E, rs79208225 (G to A), with a rate of 1% in the general population and 9% in HCC patients. Also, the SNP was shown to affect splicing, leading to a decrease in NELF-E mRNA expression. Thus, our hypothesis was HCC patients with the NELF-E SNP would have better overall outcomes and, by biologically mimicking the SNP, we could improve tumor burden. Methods: Genomic DNA from a diverse patient population was analyzed between 2016 and 2021 from our institution. Sanger sequencing was performed to detect the SNP. T-tests, Kaplan-Meier, and Cox regression analyses were performed on patients with clinical data to characterize differences between SNP and non-SNP HCC patients (STATA 17). Additionally, three HCC cell lines were treated with anti-sense oligonucleotides (ASOs) designed to mimic the splicing effects associated with the SNP. Using polymerase chain reaction (PCR), western blot, and xCELLigence real-time cell analysis, RNA and protein expression as well as proliferation was compared after treatment. Results: The rs79208225 SNP was found in 3.8% of patients in our population (8/208). Of interest, Chinese patients were more likely to have the SNP compared to other races (OR 3.38, 95% CI: 1.002-11.4, p=0.05). All SNP patients’ causative etiology was HBV. No correlation was found between age and sex. Patients with the SNP survived significantly longer (52.8 v 30.5 months, p=0.02) and had significantly longer time to recurrence (52.8 v 25.0 months, p=0.001) after surgical resection. After treatment with the ASOs, we found significantly reduced wild-type NELF-E mRNA and protein expression, consistent with HCC patient samples. Moreover, cell proliferation of HCC cells treated with the two ASOs significantly decreased compared to control. Conclusions: There is a correlative relationship between race, etiology, and improved outcomes in HCC patients with the SNP. Specifically, in patients with the SNP, survival was on average 22.3 months longer and disease-free survival was 27.8 months longer. ASOs can be used to mimic the beneficial phenotype seen in patients who carry the mutation. Further studies will include in vivo studies using the ASOs and expanding work determining the clinical significance of the SNP in HCC patients. Citation Format: Ryan Lamm, Anna Barry-Wolbers, Kai Zhang, Keyur Patel, Hien T. Dang. Clinical significance of a negative elongation factor-E (NELF-E) single nucleotide polymorphism in hepatocellular carcinoma (HCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 508.